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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGACGAACTTGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactttgggtctttgtgtattatactgctccctcttttgttcatagattgctcgccaaattatttatatattttcctgtgaattttttcttgttcccttgtataattacttgcccattgtatttaaattgatgtgctgaaccacttgaatgcttctttgcccttgcag

Basic information

species Oryza sativa
transcript LOC_Os06g01700.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01700.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G154278_T02 (Zea mays), 5'ss of exon 2
GGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGACGAACTTGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactttgggtctttgtgtattatactgctccctcttttgttcatagattgctcgccaaattatttatatattttcctgtgaattttttcttgttcccttgtataattacttgcccattgtatttaaattgatgtgctgaaccacttgaatgcttctttgcccttgcag
|| ||||| |||||||| |||||||||||||||||||||||||| ||||||||||| |||||| | ||||||||||| || ||||| |||||||||||||||| |  ||     | | | ||| |  | ||  |   |||    ||||  |||   |  | |  |  | | || | || | | | ||| | |   |  |  | |  |                                                                  
GGTCAACAGACCCAAGAGGAGTTACAGAAGAGGAATCTCAGGGAGGAACTTGAGGAACGTGAGCGCAAGCACTACTCTTCCAAGGATAAGTCCTATGCTGgta-tggctac---tttctctgtctcgttct-tttgttctccccttca-ggataagtttctagctggtatgtacaattac-tatcaatatgtatcttctttcctacag-----------------------------------------------------------------

upper sequence: LOC_Os06g01700.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G062076_T02 (Zea mays), 5'ss of exon 2
GGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGACGAACTTGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactttgggtctttgtgtattatactgctccctcttttgttcatagattgctcgccaaattatttatatattttcctgtgaattttttcttgttcccttgtataattacttgcccattgtatttaaattgatgtgctgaaccacttgaatgcttctttgcccttgcag
|| ||||| |||||||| |||||||||||||||||||||||||| ||||||||||| |||||| | ||||||||||| || ||||| ||||||||||| |||||  || |    | | | ||| |  |   | |     |     |  | |||      |  | |  | | || | |        |  | | |||  || ||| | |                                                                  
GGTCAACAGACCCAAGAGGAGTTACAGAAGAGGAATCTCAGGGAGGAACTTGAGGAACGTGAGCGCAAGCACTACTCTTCCAAGGATAAGTCCTATGCCGgtac--acct--attttctctgtctcgt-tcgtttgtgttaccccttctggataagattctgattggtatgtacaatcagtaacaatatgtatctccttgcct-gcag-----------------------------------------------------------------

upper sequence: LOC_Os06g01700.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G154278_T01 (Zea mays), 5'ss of exon 2
GGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGACGAACTTGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactttgggtctttgtgtattatactgctccctcttttgttcatagattgctcgccaaattatttatatattttcctgtgaattttttcttgttcccttgtataattacttgcccattgtatttaaattgatgtgctgaaccacttgaatgcttctttgcccttgcag
|| ||||| |||||||| |||||||||||||||||||||||||| ||||||||||| |||||| | ||||||||||| || ||||| |||||||||||||||| |  ||     | | | ||| |  | ||  |   |||    ||||  |||   |  | |  |  | | || | || | | | ||| | |   |  |  | |  | ||                                                               
GGTCAACAGACCCAAGAGGAGTTACAGAAGAGGAATCTCAGGGAGGAACTTGAGGAACGTGAGCGCAAGCACTACTCTTCCAAGGATAAGTCCTATGCTGgta-tggctac---tttctctgtctcgttct-tttgttctccccttca-ggataagtttctagctggtatgtacaattac-tatcaatatgtatcttctttcctacagaag--------------------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88420938|gb|CI620256.1|CI620256
EST:     TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTG                         AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
genomic: TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
EST: gi|88402391|gb|CI596252.1|CI596252
EST:     TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTG                         AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
genomic: TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
EST: gi|86831590|gb|CI301440.1|CI301440
EST:     TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTG                         AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCC
genomic: TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCC
EST: gi|88573290|gb|CI664861.1|CI664861
EST:     TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTG                         AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
genomic: TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
EST: gi|88742245|gb|CI765753.1|CI765753
EST:     TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTG                         AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAGGTTCAAGG
genomic: TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAGGTTCAAGG
EST: gi|88427649|gb|CI689512.1|CI689512
EST:     TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTG                         AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
genomic: TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
EST: gi|88444118|gb|CI594491.1|CI594491
EST:     TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTG                         AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTACAAG
genomic: TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
EST: gi|88743536|gb|CI767044.1|CI767044
EST:     TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTG                         AGGAGAGAGATAGGCG
genomic: TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCG
EST: gi|88301238|gb|CI594764.1|CI594764
EST:     TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTG                         AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
genomic: TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
EST: gi|88402420|gb|CI596281.1|CI596281
EST:     TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTG                         AGGAGAGAGATAGGCGGAAAAGCATAAGCCTACTCCTAGAAG
genomic: TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
EST: gi|88377322|gb|CI600477.1|CI600477
EST:     TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTG                         AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
genomic: TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
EST: gi|88339685|gb|CI660475.1|CI660475
EST:     TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTG                         AGGAGAGAGATAGGCGGAAAAGC
genomic: TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCGGAAAAGC
EST: gi|88342051|gb|CI644388.1|CI644388
EST:     TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTG                         AGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG
genomic: TGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 75 (downstream exon)
Score: 195

GGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGACGAACTTGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactt ... gcccttgcagAGGAGAGAGATAGGCGGAAAAGCACAAGCCTACTCCTAGAAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGACGAACTTGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCCTATGCTGgtactaactttgggtctttgtgtattatactgctccctcttttgttcatagattgctcgccaaattatttatatattttcctgtgaattttttcttgttcccttgtataattacttgcccattgtatttaaattgatgtgctgaaccacttgaatgcttctttgcccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG